KNOS3_ORYSJ
ID KNOS3_ORYSJ Reviewed; 314 AA.
AC Q94LW3; A0A0P0VSE3; B9FAU3; Q0DVL9; Q10SG6; Q8H8G5; Q8H8G6; Q9SXN1;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 25-MAY-2022, entry version 132.
DE RecName: Full=Homeobox protein knotted-1-like 3;
DE AltName: Full=Homeobox protein HOS66;
GN Name=HOS66; OrderedLocusNames=Os03g0123500, LOC_Os03g03164;
GN ORFNames=OJ1126B12.15/OJ1126B12.16, OsJ_008895, OsJ_008896, OsJ_09228;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), AND TISSUE SPECIFICITY.
RC STRAIN=cv. Nipponbare;
RX PubMed=12034492; DOI=10.1016/s0378-1119(02)00460-2;
RA Ito Y., Hirochika H., Kurata N.;
RT "Organ-specific alternative transcripts of KNOX family class 2 homeobox
RT genes of rice.";
RL Gene 288:41-47(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP DEVELOPMENTAL STAGE.
RX PubMed=10095070; DOI=10.1016/s0167-4781(99)00023-8;
RA Ito Y., Eiguchi M., Kurata N.;
RT "Expression of novel homeobox genes in early embryogenesis in rice.";
RL Biochim. Biophys. Acta 1444:445-450(1999).
RN [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18430022; DOI=10.1111/j.1742-4658.2008.06424.x;
RA Jain M., Tyagi A.K., Khurana J.P.;
RT "Genome-wide identification, classification, evolutionary expansion and
RT expression analyses of homeobox genes in rice.";
RL FEBS J. 275:2845-2861(2008).
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00108,
CC ECO:0000255|PROSITE-ProRule:PRU00559}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q94LW3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q94LW3-2; Sequence=VSP_036178, VSP_036179;
CC -!- TISSUE SPECIFICITY: Isoform 1 is expressed in roots and flowers, and at
CC lower levels in leaf blades and leaf sheaths. Isoform 2 is expressed in
CC roots and flowers. {ECO:0000269|PubMed:12034492}.
CC -!- DEVELOPMENTAL STAGE: Expressed in embryo at 3 days after pollination
CC (DAP). {ECO:0000269|PubMed:10095070}.
CC -!- SIMILARITY: Belongs to the TALE/KNOX homeobox family.
CC {ECO:0000255|PROSITE-ProRule:PRU00559}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN74840.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
CC Sequence=AAN74841.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
CC Sequence=ABF93721.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF10719.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=EEE58243.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB061819; BAB55660.1; -; mRNA.
DR EMBL; AB007629; BAA77823.1; -; mRNA.
DR EMBL; AC098695; AAN74840.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC098695; AAN74841.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF93720.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF93721.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF93722.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF93723.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF10719.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; BAS82051.1; -; Genomic_DNA.
DR EMBL; CM000140; EEE58243.1; ALT_INIT; Genomic_DNA.
DR RefSeq; XP_015628919.1; XM_015773433.1. [Q94LW3-1]
DR AlphaFoldDB; Q94LW3; -.
DR SMR; Q94LW3; -.
DR STRING; 4530.OS03T0123500-02; -.
DR PaxDb; Q94LW3; -.
DR EnsemblPlants; Os03t0123500-02; Os03t0123500-02; Os03g0123500. [Q94LW3-1]
DR GeneID; 4331449; -.
DR Gramene; Os03t0123500-02; Os03t0123500-02; Os03g0123500. [Q94LW3-1]
DR KEGG; osa:4331449; -.
DR eggNOG; KOG0773; Eukaryota.
DR InParanoid; Q94LW3; -.
DR OMA; DISSMMI; -.
DR OrthoDB; 1070344at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q94LW3; baseline and differential.
DR Genevisible; Q94LW3; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0010192; P:mucilage biosynthetic process; IEA:EnsemblPlants.
DR GO; GO:0080001; P:mucilage extrusion from seed coat; IEA:EnsemblPlants.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IEA:EnsemblPlants.
DR GO; GO:2000652; P:regulation of secondary cell wall biogenesis; IEA:EnsemblPlants.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0010214; P:seed coat development; IEA:EnsemblPlants.
DR GO; GO:0080112; P:seed growth; IEA:EnsemblPlants.
DR GO; GO:0010089; P:xylem development; IEA:EnsemblPlants.
DR CDD; cd00086; homeodomain; 1.
DR InterPro; IPR005539; ELK_dom.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR008422; Homeobox_KN_domain.
DR InterPro; IPR005540; KNOX1.
DR InterPro; IPR005541; KNOX2.
DR Pfam; PF05920; Homeobox_KN; 1.
DR Pfam; PF03790; KNOX1; 1.
DR Pfam; PF03791; KNOX2; 1.
DR SMART; SM00389; HOX; 1.
DR SMART; SM01255; KNOX1; 1.
DR SMART; SM01256; KNOX2; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS51213; ELK; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA-binding; Homeobox; Nucleus; Reference proteome.
FT CHAIN 1..314
FT /note="Homeobox protein knotted-1-like 3"
FT /id="PRO_0000360006"
FT DOMAIN 218..238
FT /note="ELK"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00559"
FT DNA_BIND 239..302
FT /note="Homeobox; TALE-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT VAR_SEQ 1..118
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12034492"
FT /id="VSP_036178"
FT VAR_SEQ 119..120
FT /note="FL -> MQ (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12034492"
FT /id="VSP_036179"
SQ SEQUENCE 314 AA; 34607 MW; 933439D9EE7C2382 CRC64;
MQGGDHGGME MGVGSFTGGG GGGECSSSSA TAAAAAAAAA AAAAAEAEER QLLKGEIAVH
PLCEQLVAAH VGCLRVATPI DHLPLIDAQL AQSSGLLHSY AAHHRPFLSP HDKQELDSFL
AQYMMLLCSF REQLQQHVRV HAVEAVMACR EIEQSLQDLT GATLEEGTGA TMSEDEDETA
PMLEGPMDMG SDGHDLMGFG PLMPTDSERS LMERVRQELK IELKQGFKSR IEDVREEILR
KRRAGKLPGD TTTILKQWWQ QHSKWPYPTE DDKAKLVEET GLQLKQINNW FINQRKRNWH
NNSQTSTLKS KRKR
